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   author = "A. Zharkikh",
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% Amino acid replacement models

% Blosum62
@article{henikoff1992,
  title={Amino acid substitution matrices from protein blocks},
  author={Henikoff, Steven and Henikoff, Jorja G},
  journal={Proceedings of the National Academy of Sciences},
  volume={89},
  number={22},
  pages={10915--10919},
  year={1992},
  publisher={National Acad Sciences}
}

% CpREV
@article{adachi2000,
  title={Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA},
  author={Adachi, Jun and Waddell, Peter J and Martin, William and Hasegawa, Masami},
  journal={Journal of Molecular Evolution},
  volume={50},
  number={4},
  pages={348--358},
  year={2000},
  publisher={Springer}
}

% Dayhoff
@inproceedings{dayhoff1978,
  title={A model of evolutionary change in proteins},
  author={Dayhoff, Margaret O and Schwartz, Robert M},
  booktitle={In Atlas of protein sequence and structure},
  year={1978},
  organization={Citeseer}
}

% DcMut
@article{kosiol2005,
  title={Different versions of the Dayhoff rate matrix},
  author={Kosiol, Carolin and Goldman, Nick},
  journal={Molecular biology and evolution},
  volume={22},
  number={2},
  pages={193--199},
  year={2005},
  publisher={SMBE}
}

% FLU
@article{dang2010,
  title={FLU, an amino acid substitution model for influenza proteins},
  author={Dang, Cuong C and Le, Quang S and Gascuel, Olivier and Le, Vinh S},
  journal={BMC evolutionary biology},
  volume={10},
  number={1},
  pages={99},
  year={2010},
  publisher={BioMed Central Ltd}
}

% HIVbw
@article{nickle2007,
  title={HIV-specific probabilistic models of protein evolution},
  author={Nickle, David C and Heath, Laura and Jensen, Mark A and Gilbert, Peter B and Mullins, James I and Pond, SL Kosakovsky},
  journal={PLoS One},
  volume={2},
  number={6},
  pages={e503},
  year={2007},
  publisher={Public Library of Science}
}

% JTT
@article{jones1992,
  title={The rapid generation of mutation data matrices from protein sequences},
  author={Jones, David T and Taylor, William R and Thornton, Janet M},
  journal={Computer applications in the biosciences: CABIOS},
  volume={8},
  number={3},
  pages={275--282},
  year={1992},
  publisher={Oxford Univ Press}
}

% LG
@article{le2008,
  title={An improved general amino acid replacement matrix},
  author={Le, Si Quang and Gascuel, Olivier},
  journal={Molecular biology and evolution},
  volume={25},
  number={7},
  pages={1307--1320},
  year={2008},
  publisher={SMBE}
}

%LG4M/LG4X
@article{le2012,
  title={Modeling protein evolution with several amino acid replacement matrices depending on site rates},
  author={Le, Si Quang and Dang, Cuong Cao and Gascuel, Olivier},
  journal={Molecular biology and evolution},
  pages={mss112},
  year={2012},
}

% MtArt
@article{abascal2007,
  title={MtArt: a new model of amino acid replacement for Arthropoda},
  author={Abascal, Federico and Posada, David and Zardoya, Rafael},
  journal={Molecular biology and evolution},
  volume={24},
  number={1},
  pages={1--5},
  year={2007},
  publisher={SMBE}
}

% MtZoa
@article{rota2009,
  title={MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies},
  author={Rota-Stabelli, Omar and Yang, Ziheng and Telford, Maximilian J},
  journal={Molecular phylogenetics and evolution},
  volume={52},
  number={1},
  pages={268--272},
  year={2009},
  publisher={Academic Press}
}

% PMB
@article{veerassamy2003,
  title={A transition probability model for amino acid substitutions from blocks},
  author={Veerassamy, Shalini and Smith, Andrew and Tillier, Elisabeth RM},
  journal={Journal of Computational Biology},
  volume={10},
  number={6},
  pages={997--1010},
  year={2003},
  publisher={Mary Ann Liebert, Inc.}
}

% RtREV
@article{dimmic2002,
  title={rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny},
  author={Dimmic, Matthew W and Rest, Joshua S and Mindell, David P and Goldstein, Richard A},
  journal={Journal of molecular evolution},
  volume={55},
  number={1},
  pages={65--73},
  year={2002},
  publisher={Springer}
}

% VT
@article{muller2000,
  title={Modeling amino acid replacement},
  author={M{\"u}ller, Tobias and Vingron, Martin},
  journal={Journal of Computational Biology},
  volume={7},
  number={6},
  pages={761--776},
  year={2000},
  publisher={Mary Ann Liebert, Inc.}
}

% WAG
@article{whelan2001,
  title={A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach},
  author={Whelan, Simon and Goldman, Nick},
  journal={Molecular biology and evolution},
  volume={18},
  number={5},
  pages={691--699},
  year={2001},
  publisher={SMBE}
}

% mtREV
@article{adachi1996,
  title={Model of amino acid substitution in proteins encoded by mitochondrial DNA},
  author={Adachi, Jun and Hasegawa, Masami},
  journal={Journal of molecular evolution},
  volume={42},
  number={4},
  pages={459--468},
  year={1996},
  publisher={Springer}
}

% mtMam
@article{yang1998,
  title={Synonymous and nonsynonymous rate variation in nuclear genes of mammals},
  author={Yang, Ziheng and Nielsen, Rasmus},
  journal={Journal of molecular evolution},
  volume={46},
  number={4},
  pages={409--418},
  year={1998},
  publisher={Springer}
}

@article{liu2014,
  title={Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias},
  author={Liu, Yang and Cox, Cymon J and Wang, Wei and Goffinet, Bernard},
  journal={Systematic biology},
  volume={63},
  number={6},
  pages={862--878},
  year={2014},
  publisher={Oxford University Press}
}
